def _build_system(mol, constrained):
if constrained:
parsley = ForceField("openff-1.0.0.offxml")
else:
parsley = ForceField("openff_unconstrained-1.0.0.offxml")
mol = Molecule.from_file(get_data_file_path("molecules/" + mol),
file_format="sdf")
if type(mol) == Molecule:
off_top = mol.to_topology()
positions = mol.conformers[0]
elif type(mol) == list:
# methane_multiconformer case is a list of two mols
off_top = Topology()
for mol_i in mol:
off_top.add_molecule(mol_i)
positions = (np.vstack([mol[0].conformers[0], mol[1].conformers[0]]) *
unit.angstrom)
from openff.toolkit.utils.toolkits import (
AmberToolsToolkitWrapper,
RDKitToolkitWrapper,
ToolkitRegistry,
)
toolkit_registry = ToolkitRegistry(
toolkit_precedence=[RDKitToolkitWrapper, AmberToolsToolkitWrapper])
omm_sys = parsley.create_openmm_system(off_top,
toolkit_registry=toolkit_registry)
return omm_sys, positions, off_top
def test_to_file_vsites(self):
"""
Checks that Topology.to_file() doesn't write vsites
"""
from tempfile import NamedTemporaryFile
from openff.toolkit.topology import Molecule, Topology
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
carbons = [atom for atom in mol.atoms if atom.atomic_number == 6]
positions = mol.conformers[0]
mol.add_bond_charge_virtual_site(
(carbons[0], carbons[1]),
0.1 * unit.angstrom,
charge_increments=[0.1, 0.05] * unit.elementary_charge,
)
topology = Topology()
topology.add_molecule(mol)
count = 0
# The file should be printed out with 9 atoms and 0 virtualsites, so we check to ensure that thtere are only 9 HETATM entries
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, positions)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM"):
count = count + 1
assert count == 9
def test_topology_virtualsites_atom_indexing(self):
"""
Add multiple instances of the same molecule, but in a different
order, and ensure that virtual site particles are indexed correctly
"""
topology = Topology()
topology.add_molecule(create_ethanol())
topology.add_molecule(create_ethanol())
topology.add_molecule(create_reversed_ethanol())
# Add a virtualsite to the reference ethanol
for ref_mol in topology.reference_molecules:
atoms = [ref_mol.atoms[i] for i in [0, 1]]
ref_mol._add_bond_charge_virtual_site(
atoms,
0.5 * unit.angstrom,
)
virtual_site_topology_atom_indices = [(0, 1), (9, 10), (26, 25)]
for top_vs, expected_indices in zip(
topology.topology_virtual_sites,
virtual_site_topology_atom_indices):
assert (tuple([at.topology_particle_index
for at in top_vs.atoms]) == expected_indices)
assert top_vs.atom(
0).topology_particle_index == expected_indices[0]
assert top_vs.atom(
1).topology_particle_index == expected_indices[1]
def test_get_virtual_site(self):
"""Test Topology.virtual_site function (get virtual site from index)"""
topology = Topology()
topology.add_molecule(self.ethane_from_smiles_w_vsites)
assert topology.n_topology_virtual_sites == 2
topology.add_molecule(self.propane_from_smiles_w_vsites)
assert topology.n_topology_virtual_sites == 4
with self.assertRaises(Exception) as context:
topology_vsite = topology.virtual_site(-1)
with self.assertRaises(Exception) as context:
topology_vsite = topology.virtual_site(4)
topology_vsite1 = topology.virtual_site(0)
topology_vsite2 = topology.virtual_site(1)
topology_vsite3 = topology.virtual_site(2)
topology_vsite4 = topology.virtual_site(3)
assert topology_vsite1.type == "BondChargeVirtualSite"
assert topology_vsite2.type == "MonovalentLonePairVirtualSite"
assert topology_vsite3.type == "MonovalentLonePairVirtualSite"
assert topology_vsite4.type == "BondChargeVirtualSite"
n_equal_atoms = 0
for topology_atom in topology.topology_atoms:
for vsite in topology.topology_virtual_sites:
for vsite_atom in vsite.atoms:
if topology_atom == vsite_atom:
n_equal_atoms += 1
# There are four virtual sites -- Two BondCharges with 2 atoms, and two MonovalentLonePairs with 3 atoms
assert n_equal_atoms == 10
def test_topology_virtual_site_particle_start_index(self):
topology = Topology()
topology.add_molecule(self.propane_from_smiles_w_vsites)
assert topology.virtual_site(
0).topology_virtual_particle_start_index == 11
assert topology.virtual_site(
1).topology_virtual_particle_start_index == 13
def test_n_topology_atoms(self):
"""Test n_atoms function"""
topology = Topology()
assert topology.n_topology_atoms == 0
assert topology.n_topology_bonds == 0
topology.add_molecule(self.ethane_from_smiles)
assert topology.n_topology_atoms == 8
assert topology.n_topology_bonds == 7
def test_is_bonded(self):
"""Test Topology.virtual_site function (get virtual site from index)"""
topology = Topology()
topology.add_molecule(self.propane_from_smiles_w_vsites)
topology.assert_bonded(0, 1)
topology.assert_bonded(1, 0)
topology.assert_bonded(1, 2)
# C-H bond
topology.assert_bonded(0, 4)
with self.assertRaises(Exception) as context:
topology.assert_bonded(0, 2)
def test_topology_virtual_site_n_particles(self):
"""
Test if the virtual sites report the correct number of particles
"""
topology = Topology()
topology.add_molecule(self.propane_from_smiles_w_vsites)
assert topology.virtual_site(0).n_particles == 2
assert topology.virtual_site(1).n_particles == 1
topology = Topology()
topology.add_molecule(self.tip5_water)
assert topology.virtual_site(0).n_particles == 2
def test_n_topology_virtual_sites(self):
"""Test n_atoms function"""
topology = Topology()
assert topology.n_topology_virtual_sites == 0
topology.add_molecule(self.ethane_from_smiles_w_vsites)
assert topology.n_topology_virtual_sites == 2
topology = Topology()
assert topology.n_topology_virtual_sites == 0
topology.add_molecule(self.tip5_water)
assert topology.n_topology_virtual_sites == 1
assert topology.n_topology_particles == 5
def test_to_file_multi_molecule_different_order(self):
"""
Checks for the following if Topology.to_write maintains the order of atoms
for the same molecule with different indexing
"""
from tempfile import NamedTemporaryFile
from openff.toolkit.tests.test_forcefield import (
create_ethanol,
create_reversed_ethanol,
)
from openff.toolkit.topology import Molecule, Topology
topology = Topology()
topology.add_molecule(create_ethanol())
topology.add_molecule(create_reversed_ethanol())
mol = Molecule.from_pdb_and_smiles(
get_data_file_path("systems/test_systems/1_ethanol.pdb"), "CCO")
positions = mol.conformers[0]
# Make up coordinates for the second ethanol by translating the first by 10 angstroms
# (note that this will still be a gibberish conformation, since the atom order in the second molecule is different)
positions = np.concatenate(
[positions, positions + 10.0 * unit.angstrom])
element_order = []
with NamedTemporaryFile(suffix=".pdb") as iofile:
topology.to_file(iofile.name, positions)
data = open(iofile.name).readlines()
for line in data:
if line.startswith("HETATM"):
element_order.append(line.strip()[-1])
assert element_order == [
"C",
"C",
"O",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"O",
"C",
"C",
]